Structure & Shape of Organic Molecules

4.1

Functional Groups

Alkane (alkyl): single C–C bond

Alkene (alkenyl): double C=C bond

Alkyne (alkynyl): triple C≡C bond

Aromatic compound (aryl): benzene ring

• Alkyl halide (halo) R – X

• Alcohol R – OH

• Ether R – O – R

• Amine R – NH₃ (primary, secondary R – NH – R, tertiary R – N – R₂ )

• Thiol R – SH (smell bad)

• Sulfide R – S – R

• Nitro compound R – NO₂

• Aldehyde (doubled bonded O at the end of a chain)

• Ketone (double bonded O in the middle of the chain)

• Carboxylic Acid (double bonded O and 1 H bond)

• Ester (double bonded O and ether (O link) group)

• Amide (double bonded O and an N group)

4.2

Infrared Spectroscopy

• IR light excites nuclear vibrations in a molecule

• Different functional groups, and structures of the molecules absorb IR light at different frequencies

Energy Absorption

• Due to quantum theory, energy levels in atoms are quantized, therefore a molecule can only exist in certain vibrational states

• The difference in energy between the ground & excited states is equal to the energy absorbed

• Wavenumber (cm^-1) (ν), used because they have value in a more manageable range

• When a molecule absorbs IR light at the proper wavelength(/wavenumber) the bonds are excited, not the electrons (excited e^- cause UV/visible light)

• Energy in the 5-50 kJ mol^-1 range

Types of Vibration

1. Stretching Vibrations:
   - Symmetric Stretching: both arms stretch out
   - Asymmetric Stretching: one arm stretches while one condenses, vv

2. Bending Vibrations:
   - Scissoring: arms move inward (like scissors)
   - Rocking: side-to-side
   - Wagging: back & forth
   - Twisting: arms twist

• Fingerprint Region: 1500-500cm^-1, very complex pattern but unique to compounds

• Functional Group Region: 4000-1500cm^-1, useful for identifying functional groups

Harmonic Oscillator

• Molecular bonds can be thought of balls and spring that vibrate

• Bond stretches & compresses more but average bond length remains the same

, where v= frequency, k= force constant, μ= reduced mass (kg)

• Stronger bonds vibrate at higher frequencies (wavenumbers)

• Triple bonds > double bonds > single bonds

• Hybridization: sp > sp² > sp³

• Mass difference: bonds of higher masses vibrate at lower frequencies

  1. Vibrational frequency of an A – X bond decreases with increasing atomic mass of X (as m₂ ↑, μ ↑)

• Alcohols have a wide, deep peak

• Carbonyls have an overtone ~3500cm^-1, echo of the C=O stretch (close to fingerprint)

4.3

Alkanes

• Saturated hydrocarbons, only single bonds

• C_nH_2n+2

• Homologous series: structurally related

• The bigger the molecules, the higher the boiling point (dispersion forces are stronger)

• C₁-C₄= gases, C₅-C₁₇=liquids, C>17 = solids or waxes @ room temp.

Constitutional Isomers: same molecular formula, different bonding sequence (connectivity)

3D Structures

1. Dot-line-wedge: dotted line goes into the page; wedge comes out of the page

2. Newman projections: looks down the C – C axis

   1. Eclipsed conformation: front atoms cover back atoms (less stable)

   2. Staggered conformation: rotated 60º

Conformations: non-permanent spatial arrangements of atoms by rotation about single bonds

Relative Energies of Conformations:

• Dihedral angle: angle between methyl groups

• Lower energy if the dihedral angle is larger because charges repel

• Gauche is to the left (or right), right next the atom

• Most stable is staggered anti (methyl groups are as far as possible)

• “steric strain/hinderance” replusive forces between molecules

Cycloalkanes: C_nH_2n because 2 H atoms were removed to close the ring

• Cyclopropane (60º) are highly strained because all C – H bonds have a eclipse conformation

• Cyclobutane (~90º) & Cyclopentane (~109.5º) are puckered (reduces repulsion of adjacent eclipsed C – H bonds & lowers strain)

• Cyclohexane (109.5º, sp³ hybrids)

  1. Boat Conformation: base of the base Cs are eclipsed, uncommon
     due to flagpole interactions (peaks interact)

  2. Chair Conformation: all C – H bonds are staggered & no flagpole
     interactions, therefore lower energy

• Axial Substituents: point straight up or down

• Equatorial Substituents: point laterally (outward)

  1. If you change which C is the top peak in a chair conformation, all the axial substituents become equatorial, & eq 🡪 axial

  2. Change if there are axial substituents repelling each other (steric repulsion), equatorial makes them further away, more energetically stable

  3. Change rapidly interconvert 🡪 not isomers

Constitutional Isomerism in Cycloalkanes

• Cis/trans isomers: non-hydrogen substituents on different Cs occupy different positions relative to the plane of the ring

• Cis: both on the same side

• Trans: opposite sides of the ring

  1. Affects properties of the molecule

Stereoisomers: same molecular formula, same bonding sequence (connectivity), different non-interconverting 3D structures

• Oriented differently in space, cannot be interconverted by rotations around single bonds

• Can’t have cis/trans isomers if there is ambiguity (don’t know which substituent to compare to)

Alkenes & Alkynes

• Unsaturated, 1/more double bonds

• Alkene C=C (C_nH_2n)

• Alkynes C≡C (C_nH_2n-2)

• For every 2 H atoms removed, 1 “unit of unsaturation”, each unit of unsaturation could be a π bond of a ring

• Each C involved in C=C bond is bonded to 2 atoms & is sp² (trigonal planar 120º)

• Each C involved in C≡C bond is bonded to 2 atoms & is sp (linear 180º)

Stereoisomerism in Alkenes

• No rotation about the π bond, therefore cis/trans may occur

• Rings with 7 members/less, a double bond within the ring can have only the cis geometry because the trans would be too strained

• Possible number of cis/trans isomers= 2ⁿ, where n is the # of bonds with 2 different substituents on each C

Vitamin A

• In the body, as retinal (Vitamin A aldehyde), deficiency causes blindness

• Retinal contains chain of 4 C=C bonds in trans configuration

• An enzyme breaks down the C=C bond & then restores the C=C in cis conf.

• Cis-retinal allows vision, when light hits cells in reconverts & cycle continues

E,Z Nomenclature for Alkene Stereoisomers

• Uses priorities to identity which substituents are cis/trans

• E is opposite, Z is same side

• RULES:

  1. Higher priority to higher atomic number

  2. If there’s a tie… continue down the chain to determine the highest out of those 2 sets

  3. Multiple bonds are given single bond equivalencies (double bond is treated as 2 single bonds)

4.4

Chirality

• Chiral objects: not superimposable, mirror images, no plane of symmetry

• Achiral objects: superimposable, same object

Enantiomers

• 2 molecules that have the same molecular formula & bonding sequence but not superimposable (mirror images)

• type of stereoisomer

• exist in pairs

Stereocenters (Chiral Centers)

• an atom bonded to 4 different groups in a tetrahedral geometry

• most common is a chiral carbon

* if you switch any 2 groups @ a chiral center you get the mirror image,
if there are 2 chiral centers in the molecule you have to switch both

Fisher Projections

• 3D structure of molecules

• “hug me but don’t kiss me”

• tetrahedral shape from a different perspective

• useful for chiral carbons

R & S Designation of Enantiomer Configuration

• assign priority using same rules as E,Z

• orient molecule so that lowest priority group is behind the plane

• direction of rotation can be R or S

• R is clockwise, S is counterclockwise

Chirality in Biomolecules

• Many physiologically active molecules exist as enantiomers

• Enantiomers behave very differently (“life or death”)

Thalidomide

• Anti-morning sickness drug in 1960s

• The R form had the desire anti-nausea effect

• The S form caused birth defects

Number of Stereosiomers

• The maximum # of stereoisomers in a molecules with n stereocenters is 2ⁿ

• Molecules can exhibit cis/trans and R,S stereoisomerism simultaneously

Plane-Polarized Light & Optical Activity

• When all waves oscillate in the same plane, light is said to be plane-polarized

• Achiral molecules have no effect

• Chiral molecules rotate the plane of polarization (are “optically active”)

• Clockwise (right) + is dextrorotation (d–)

• Counterclockwise (left) – is laevorotation (l–)

• D/L is based on how fisher projections are drawn

Same Formula

Same Connectivity Different Connectivity
∴ same molecule ∴ constitutional isomers

Different non-interconverting same non-interconverting

spatial arrangement spatial arrangement

∴ stereoisomers ∴ not stereoisomers